Trapped Be+ ions are a leading platform for quantum information science [1], but reactions with background gas species, such as H2 and H2O, result in qubit loss. Our experiment reveals that the BeOH+ ion is the final trapped ion species when both H2 and H2O exist in a vacuum system with cold, trapped Be+. To understand the loss mechanism, low-temperature reactions between sympathetically cooled BeD+ ions and H2O molecules have been investigated using an integrated, laser-cooled Be+ ion trap and high-resolution Time-of-Flight (TOF) mass spectrometer (MS) [2]. Among all the possible products,BeH2O+, H2DO+, BeOD+, and BeOH+, only the BeOH+ molecular ion was observed experimentally, with the assumed co-product of HD. Theoretical analyses based on explicitly correlated restricted coupled cluster singles, doubles, and perturbative triples (RCCSD(T)-F12) method with the augmented correlation-consistent polarized triple zeta (AVTZ) basis set reveal that two intuitive direct abstraction product channels, Be + H2DO+ and D + BeH2O+, are not energetically accessible at the present reaction temperature (~150 K). Instead, a double displacement BeOH+ + HD product channel is accessible due to a large exothermicity of 1.885 eV through a submerged barrier in the reaction pathway. While the BeOD+ + H2 product channel has a similar exothermicity, the reaction pathway is dynamically unfavourable, as suggested by a Sudden Vector Projection analysis. This work sheds light on the origin of the loss and contaminations of the laser-cooled Be+ ions in quantum-information experiments.